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https://github.com/haesleinhuepf/napari-process-points-and-surfaces

Process and analyze surfaces using vedo in napari.
https://github.com/haesleinhuepf/napari-process-points-and-surfaces

napari-plugin

Last synced: 23 days ago
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Process and analyze surfaces using vedo in napari.

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README 

        
# napari-process-points-and-surfaces (nppas)



[![License](https://img.shields.io/pypi/l/napari-process-points-and-surfaces.svg?color=green)](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/master/LICENSE)

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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7654555.svg)](https://doi.org/10.5281/zenodo.7654555)



Process and analyze surfaces using [vedo](https://vedo.embl.es/) in [napari].



![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/graphical_abstract.gif)

The nppas gastruloid example is derived from [AV Luque and JV Veenvliet (2023)](https://zenodo.org/record/7603081) which is licensed [CC-BY](https://creativecommons.org/licenses/by/4.0/legalcode) and can be downloaded from here: https://zenodo.org/record/7603081



## Usage



You find menus for surface generation, smoothing and analysis in the menu `Tools > Surfaces` and `Tools > Points`. 

For detailed explanation of the underlying algorithms, please refer to the [vedo](https://vedo.embl.es/) documentation.



For processing meshes in Python scripts, see the [demo notebook](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/blob/main/docs/demo.ipynb). 

There you also learn how this screenshot is made:



![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/screenshot5.png)



For performing quantitative measurements of surface in Python scripts, see the [demo notebook](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/blob/main/docs/quality_measurements.ipynb). 

There you also learn how this screenshot is made:



![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/screenshot6.png)



### Surface measurements and annotations



Using the menu `Tools > Measurement tables > Surface quality table (vedo, nppas)` you can derive quantiative measurements of

the vertices in a given surface layer. 



![img_1.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/surface_measurements2.png)



To differentiate regions when analyzing those measurements it is recommended to use the menu `Tools > Surfaces > Annotate surface manually (nppas)`

after measurements have been made. This tool allows you to draw annotation label values on the surface. 

It is recommended to do activate a colorful colormap such as `hsv` before starting to draw annotations. 

Furthermore, set the maximum of the contrast limit range to the number of regions you want to annotate + 1.

Annotations can be drawn as freehand lines and circles.



![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/surface_annotation2.png)



After measurements and annotations were done, you can save the annotation in the same measurement table using the menu

`Tools > Measurement tables > Surface quality/annotation to table (nppas)`



![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/surface_annotation_in_table2.png)



For classifying surface vertices using machine learning, please refer to the [napari APOC](https://www.napari-hub.org/plugins/napari-accelerated-pixel-and-object-classification) documentation.



### Measurement visualization



To visualize measurements on the surface, just double-click on the table column headers.



![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/quality_measurements.gif)



## Installation



You can install `napari-process-points-and-surfaces` via mamba/conda:



```

mamba install vedo=2022.4.1 napari-process-points-and-surfaces -c conda-forge

```



### Troubleshooting: Open3d installation



Since version 0.4.0, `nppas` does no longer depend on [open3d](http://www.open3d.org/). 

Some deprecated functions still use Open3d though. 

Follow the installation instructions in the [open3d documentation](http://www.open3d.org/docs/release/getting_started.htm) to install it and keep using those functions.

Also consider updating code and no longer using these deprecated functions. 

See [release notes](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/releases/tag/0.4.0) for details.



## See also



There are other napari plugins with similar / overlapping functionality

* [morphometrics](https://www.napari-hub.org/plugins/morphometrics)  

* [napari-accelerated-pixel-and-object-classification](https://www.napari-hub.org/plugins/napari-accelerated-pixel-and-object-classification)

* [napari-pymeshlab](https://www.napari-hub.org/plugins/napari-pymeshlab)

* [napari-pyclesperanto-assistant](https://www.napari-hub.org/plugins/napari-pyclesperanto-assistant)

* [napari-stress](https://www.napari-hub.org/plugins/napari-stress)

* [surforama](https://github.com/cellcanvas/surforama)



And there is software for doing similar things:

* [meshlab](https://www.meshlab.net/)

* [paraview](https://www.paraview.org/)



## Contributing



Contributions are very welcome. Tests can be run with [tox], please ensure

the coverage at least stays the same before you submit a pull request.



## License



Distributed under the terms of the [BSD-3] license,

"napari-process-points-and-surfaces" is free and open source software



## Acknowledgements



Some code snippets and example data were taken from the [vedo](https://vedo.embl.es/) and [open3d](http://www.open3d.org/) 

repositories and documentation. See [thirdparty licenses](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/tree/main/licenses_third_party) for licensing details.

The Standford Bunny example dataset has been taken from [The Stanford 3D Scanning Repository](http://graphics.stanford.edu/data/3Dscanrep/).

The nppas gastruloid example is derived from [AV Luque and JV Veenvliet (2023)](https://zenodo.org/record/7603081) which is licensed [CC-BY](https://creativecommons.org/licenses/by/4.0/legalcode) and can be downloaded from here: https://zenodo.org/record/7603081



## Issues



If you encounter any problems, please create a thread on [image.sc] along with a detailed description and tag [@haesleinhuepf].



[napari]: https://github.com/napari/napari

[Cookiecutter]: https://github.com/audreyr/cookiecutter

[@napari]: https://github.com/napari

[MIT]: http://opensource.org/licenses/MIT

[BSD-3]: http://opensource.org/licenses/BSD-3-Clause

[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt

[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt

[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0

[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt

[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin



[file an issue]: https://github.com/haesleinhuepf/napari-process-points-and-surfaces/issues



[napari]: https://github.com/napari/napari

[tox]: https://tox.readthedocs.io/en/latest/

[pip]: https://pypi.org/project/pip/

[PyPI]: https://pypi.org/



[image.sc]: https://image.sc

[@haesleinhuepf]: https://twitter.com/haesleinhuepf